A simple method for faster nonbonded force evaluations.
A simple method for faster nonbonded force evaluations.
复制标题
一种用于更快地评估非键合力的简单方法。
DOI：
10.1002/jcc.20211
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发表时间：
2005
影响因子：
3
通讯作者：
Freed,KarlF
中科院分区：
文献类型：
--
作者：
Shen,Min-Yi;Freed,KarlF
引入精确的近似值来评估粒子间距离的倒数，使得在计算粒子间相互作用和力时不需要平方根或除法运算。这些普遍适用的近似通过并入蛋白质模拟包TINKER（Pappu，R.五、哈特河K.的;思考，J.W. J Phys Chem B 1998，102，9725; Ponder，J.W.;理查兹，F. M. J Comput Chem 1987，8，1016; Dudek，M. J.道：Ramnarayan，K.;思考，J.W. J Comput Chem 1998，19，548）沿着几种其它的速度增强策略。通过这些修改，蛋白质的隐式溶剂朗之万动力学模拟比修改后的开源分布式程序快4.6倍。编程加速获得广泛的矢量化，简化的内部循环，以避免IF语句，并通过使用查找表的距离依赖的“介电常数”在隐式溶剂模型。提供了甲硫氨酸脑啡肽、绒毛蛋白头部、G蛋白B1结构域和芽孢杆菌RNA酶的全原子、隐式溶剂动力学的基准。我们还讨论了近似方法对显式溶剂模拟的更普遍的适用性，以及其他隐式溶剂模型（如广义Born模型）的查找表。© 2005 Wiley Periodicals，Inc. J Comput Chem 26：691-698，2005
Accurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER (Pappu, R. V.; Hart, R. K.; Ponder, J. W. J Phys Chem B 1998, 102, 9725; Ponder, J. W.; Richards, F. M. J Comput Chem 1987, 8, 1016; Dudek, M. J.; Ramnarayan, K.; Ponder, J. W. J Comput Chem 1998, 19, 548) along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent “dielectric constant” in implicit solvent models. Benchmarks are provided for the all‐atom, implicit solvent dynamics of Met‐enkephalin, the villin headpiece, the B1 domain of protein‐G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look‐up tables for other implicit solvent models such as the generalized Born models. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 691–698, 2005